(Q27320451)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27091704%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

title

Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27091704%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27091704%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

Lu Zhang

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27091704%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

Xin Gao

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27091704%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

author name string

Lin-Tai Da

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27091704%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

Fátima Pardo-Avila

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27091704%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

Liang Xu

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27091704%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

Daniel-Adriano Silva

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27091704%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

Dong Wang

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27091704%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

language of work or name

English

0 references

publication date

19 April 2016

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27091704%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

published in

Nature Communications

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27091704%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

volume

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27091704%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

page(s)

11244

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27091704%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

2 April 2020

copyright license

start time

19 April 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Structure of transcribing mammalian RNA polymerase II

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

Structure-guided simulations illuminate the mechanism of ATP transport through VDAC1

21 March 2017

1 reference

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Markov state models of biomolecular conformational dynamics

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

Structural basis of transcriptional pausing in bacteria

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

Active site opening and closure control translocation of multisubunit RNA polymerase

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

Structural basis of RNA polymerase II backtracking, arrest and reactivation

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

Structural Basis of Transcription: Backtracked RNA Polymerase II at 3.4 Angstrom Resolution

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

The X-ray crystal structure of RNA polymerase from Archaea

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

The molecular basis of eukaryotic transcription

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

Comparison of multiple Amber force fields and development of improved protein backbone parameters

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

GROMACS: fast, flexible, and free

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

A role for both conformational selection and induced fit in ligand binding by the LAO protein

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

Allostery through the computational microscope: cAMP activation of a canonical signalling domain

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

Five checkpoints maintaining the fidelity of transcription by RNA polymerases in structural and energetic details

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

On the Application of Molecular-Dynamics Based Markov State Models to Functional Proteins

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

The X-ray crystal structure of the euryarchaeal RNA polymerase in an open-clamp configuration

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

RNA polymerase pausing and nascent-RNA structure formation are linked through clamp-domain movement

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

Molecular basis of transcriptional fidelity and DNA lesion-induced transcriptional mutagenesis

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

Millisecond dynamics of RNA polymerase II translocation at atomic resolution

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

Complete dissection of transcription elongation reveals slow translocation of RNA polymerase II in a linear ratchet mechanism

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

Energetic and structural details of the trigger-loop closing transition in RNA polymerase II.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

To milliseconds and beyond: challenges in the simulation of protein folding

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

Dynamics of pyrophosphate ion release and its coupled trigger loop motion from closed to open state in RNA polymerase II.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

Linking RNA polymerase backtracking to genome instability in E. coli

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

RNA polymerase II with open and closed trigger loops: active site dynamics and nucleic acid translocation

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

RNA polymerase II trigger loop residues stabilize and position the incoming nucleotide triphosphate in transcription

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

Reparameterization of RNA chi Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

RNA polymerase fidelity and transcriptional proofreading

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

Rapid equilibrium sampling initiated from nonequilibrium data

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

Progress and challenges in the automated construction of Markov state models for full protein systems

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

RNA polymerase active center: the molecular engine of transcription

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

Transcriptional pausing without backtracking

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

Using generalized ensemble simulations and Markov state models to identify conformational states

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

Transition-path theory and path-finding algorithms for the study of rare events

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

Can morphing methods predict intermediate structures?

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

Building Markov state models along pathways to determine free energies and rates of transitions

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

Transition networks for modeling the kinetics of conformational change in macromolecules

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

RNA polymerase encounters with DNA damage: transcription-coupled repair or transcriptional mutagenesis?

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

Diffusion of nucleoside triphosphates and role of the entry site to the RNA polymerase II active center

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

Characterization of a novel RNA polymerase II arrest site which lacks a weak 3' RNA-DNA hybrid

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

5-formylcytosine and 5-carboxylcytosine reduce the rate and substrate specificity of RNA polymerase II transcription.

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

Atomistic folding simulations of the five-helix bundle protein λ(6−85).

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

Evidence that transcript cleavage is essential for RNA polymerase II transcription and cell viability

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

Role of the RNA polymerase trigger loop in catalysis and pausing.

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838855

Synergistic action of RNA polymerases in overcoming the nucleosomal barrier.

31 May 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS11244

RNA polymerase backtracking in gene regulation and genome instability

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS11244

Coarse master equations for peptide folding dynamics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS11244

Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS11244

Probing molecular kinetics with Markov models: metastable states, transition pathways and spectroscopic observables

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS11244

Dynamics of an intrinsically disordered protein reveal metastable conformations that potentially seed aggregation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS11244

A global geometric framework for nonlinear dimensionality reduction

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS11244

Intrinsic translocation barrier as an initial step in pausing by RNA polymerase II.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS11244

The RNA-DNA hybrid maintains the register of transcription by preventing backtracking of RNA polymerase.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS11244

Constructing kinetic models to elucidate structural dynamics of a complete RNA polymerase II elongation cycle.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS11244

Identification of slow molecular order parameters for Markov model construction

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS11244

Simulating the T-Jump-Triggered Unfolding Dynamics of trpzip2 Peptide and Its Time-Resolved IR and Two-Dimensional IR Signals Using the Markov State Model Approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS11244

21 January 2018

Identifiers

DOI

10.1038/NCOMMS11244

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27091704%20AND%20SRC:MED&resulttype=core&format=json

Dimensions Publication ID

2 April 2020

ADS bibcode

2016NatCo...711244D

0 references

1038248839

0 references

Fatcat ID

release_cdab2oweonftzcb3v54c7od2gu

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/cdab2oweonftzcb3v54c7od2gu

mapped directly with Wikidata item

24 November 2022

based on heuristic

OpenCitations bibliographic resource ID

2238378

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

2 references

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

2238378

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27091704%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

PubMed publication ID

27091704

1 reference